galaxy-commits July 2013

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commit/galaxy-central: jgoecks: Allow spaces and commas in Cuffdiff labels.
by commits-noreply＠bitbucket.org 01 Jul '13

01 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5b27b92310d0/ Changeset: 5b27b92310d0 User: jgoecks Date: 2013-07-01 15:46:09 Summary: Allow spaces and commas in Cuffdiff labels. Affected #: 1 file diff -r 5a73d78e0a4782d9c57d8c1d6cea167e4f4671b6 -r 5b27b92310d044cfd2f9b3711e5ef446048de110 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -59,7 +59,9 @@ ## Replicates. --labels #for $group in $group_analysis.groups - "${group.group}" + ## Cuffdiff uses commas as delimiters, so replace them with underscores to avoid + ## parsing problems. + "${group.group.replace(',', '_')}" #end for --files #for $group in $group_analysis.groups @@ -80,7 +82,7 @@ </param><when value="Yes"><repeat name="groups" title="Group"> - <param name="group" title="Group name" type="text" label="Group name (no spaces or commas)"/> + <param name="group" title="Group name" type="text" label="Group name"/><repeat name="files" title="Replicate"><param name="file" label="Add file" type="data" format="sam,bam"/></repeat> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Fix converter imports -- resolves failing unit tests
by commits-noreply＠bitbucket.org 01 Jul '13

01 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5a73d78e0a47/ Changeset: 5a73d78e0a47 User: dannon Date: 2013-07-01 11:57:51 Summary: Fix converter imports -- resolves failing unit tests Affected #: 2 files diff -r 6673bd3bf4571c4134797077ca85350a6319e444 -r 5a73d78e0a4782d9c57d8c1d6cea167e4f4671b6 lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_interval_index_converter.py @@ -11,15 +11,13 @@ from __future__ import division -import sys, fileinput, optparse +import optparse from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.tracks.summary import * -from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed +eggs.require( "bx-python" ) from bx.interval_index_file import Indexes def main(): - + # Read options, args. parser = optparse.OptionParser() parser.add_option( '-c', '--chr-col', type='int', dest='chrom_col', default=1 ) @@ -27,12 +25,12 @@ parser.add_option( '-e', '--end-col', type='int', dest='end_col', default=3 ) (options, args) = parser.parse_args() input_fname, output_fname = args - + # Make column indices 0-based. options.chrom_col -= 1 options.start_col -= 1 options.end_col -= 1 - + # Do conversion. index = Indexes() offset = 0 @@ -46,9 +44,9 @@ chrom_end = int( feature[ options.end_col ] ) index.add( chrom, chrom_start, chrom_end, offset ) offset += len(line) - + index.write( open(output_fname, "w") ) -if __name__ == "__main__": +if __name__ == "__main__": main() - \ No newline at end of file + diff -r 6673bd3bf4571c4134797077ca85350a6319e444 -r 5a73d78e0a4782d9c57d8c1d6cea167e4f4671b6 lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py --- a/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py +++ b/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py @@ -8,20 +8,18 @@ from __future__ import division -import sys, fileinput, optparse +import optparse from galaxy import eggs -import pkg_resources; pkg_resources.require( "bx-python" ) -from galaxy.visualization.tracks.summary import * -from galaxy.datatypes.util.gff_util import convert_gff_coords_to_bed +eggs.require( "bx-python" ) from bx.interval_index_file import Indexes def main(): - + # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() input_fname, output_fname = args - + # Do conversion. index = Indexes() offset = 0 @@ -31,9 +29,9 @@ start = int( start ) - 1 index.add( chrom, start, start + 1, offset ) offset += len( line ) - + index.write( open(output_fname, "w") ) -if __name__ == "__main__": +if __name__ == "__main__": main() - \ No newline at end of file + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 01 Jul '13

01 Jul '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/682bc706f5d6/ Changeset: 682bc706f5d6 User: jmchilton Date: 2013-06-24 16:28:14 Summary: Create unit test directory with example test. Enable coverage report generation of unit tests (run_unit_tests.sh will automatically add --with-coverage to nosetests call if coverage is on the path, coverage report can than be generated with 'coverage html' and viewed at htmlcov/index.html). Update .hgignore to reflect these changes. Affected #: 6 files diff -r dc6e0347edffb96fe4e633b362ad21a9f5a83e81 -r 682bc706f5d6c8caab7a46e405cdee158268c373 .coveragerc --- /dev/null +++ b/.coveragerc @@ -0,0 +1,3 @@ +[run] +branch = True +include = lib/galaxy/* diff -r dc6e0347edffb96fe4e633b362ad21a9f5a83e81 -r 682bc706f5d6c8caab7a46e405cdee158268c373 .hgignore --- a/.hgignore +++ b/.hgignore @@ -82,6 +82,9 @@ # Test output run_functional_tests.html test/tool_shed/tmp/* +.coverage +htmlcov +run_unit_tests.html # Project files *.kpf diff -r dc6e0347edffb96fe4e633b362ad21a9f5a83e81 -r 682bc706f5d6c8caab7a46e405cdee158268c373 lib/galaxy/tools/loader.py --- a/lib/galaxy/tools/loader.py +++ b/lib/galaxy/tools/loader.py @@ -202,199 +202,3 @@ current_index += 1 parent_el.insert(current_index, deepcopy(target)) parent_el.remove(query) - - -def test_loader(): - """ - Function to test this module. Galaxy doesn't seem to have a - place to put unit tests that are not doctests. These tests can - be run with nosetests via the following command: - - % nosetests lib/galaxy/tools/loader.py - - """ - from tempfile import mkdtemp - from shutil import rmtree - - class TestToolDirectory(object): - def __init__(self): - self.temp_directory = mkdtemp() - - def __enter__(self): - return self - - def __exit__(self, type, value, tb): - rmtree(self.temp_directory) - - def write(self, contents, name="tool.xml"): - open(os.path.join(self.temp_directory, name), "w").write(contents) - - def load(self, name="tool.xml", preprocess=True): - if preprocess: - loader = load_tool - else: - loader = parse_xml - return loader(os.path.join(self.temp_directory, name)) - - ## Test simple macro replacement. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs" /> - <macros> - <macro name="inputs"> - <inputs /> - </macro> - </macros> -</tool>''') - xml = tool_dir.load(preprocess=False) - assert xml.find("inputs") is None - xml = tool_dir.load(preprocess=True) - assert xml.find("inputs") is not None - - # Test importing macros from external files - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs" /> - <macros> - <import>external.xml</import> - </macros> -</tool>''') - - tool_dir.write(''' -<macros> - <macro name="inputs"> - <inputs /> - </macro> -</macros>''', name="external.xml") - xml = tool_dir.load(preprocess=False) - assert xml.find("inputs") is None - xml = tool_dir.load(preprocess=True) - assert xml.find("inputs") is not None - - # Test macros with unnamed yield statements. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs"> - <input name="first_input" /> - </expand> - <macros> - <macro name="inputs"> - <inputs> - <yield /> - </inputs> - </macro> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs").find("input").get("name") == "first_input" - - # Test recursive macro applications. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs"> - <input name="first_input" /> - <expand macro="second" /> - </expand> - <macros> - <macro name="inputs"> - <inputs> - <yield /> - </inputs> - </macro> - <macro name="second"> - <input name="second_input" /> - </macro> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs").findall("input")[1].get("name") == "second_input" - - # Test recursive macro applications. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs"> - <input name="first_input" /> - <expand macro="second" /> - </expand> - <macros> - <macro name="inputs"> - <inputs> - <yield /> - </inputs> - </macro> - <macro name="second"> - <expand macro="second_delegate" /> - </macro> - <macro name="second_delegate"> - <input name="second_input" /> - </macro> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs").findall("input")[1].get("name") == "second_input" - - # Test <xml> is shortcut for macro type="xml" - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs" /> - <macros> - <xml name="inputs"> - <inputs /> - </xml> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs") is not None - - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <command interpreter="python">tool_wrapper.py - #include source=$tool_params - </command> - <macros> - <template name="tool_params">-a 1 -b 2</template> - </macros> -</tool> -''') - xml = tool_dir.load() - params_dict = template_macro_params(xml.getroot()) - assert params_dict['tool_params'] == "-a 1 -b 2" - - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <macros> - <token name="@CITATION@">The citation.</token> - </macros> - <help>@CITATION@</help> - <another> - <tag /> - </another> -</tool> -''') - xml = tool_dir.load() - help_el = xml.find("help") - assert help_el.text == "The citation.", help_el.text - - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <macros> - <token name="@TAG_VAL@">The value.</token> - </macros> - <another> - <tag value="@TAG_VAL@" /> - </another> -</tool> -''') - xml = tool_dir.load() - tag_el = xml.find("another").find("tag") - value = tag_el.get('value') - assert value == "The value.", value diff -r dc6e0347edffb96fe4e633b362ad21a9f5a83e81 -r 682bc706f5d6c8caab7a46e405cdee158268c373 run_unit_tests.sh --- a/run_unit_tests.sh +++ b/run_unit_tests.sh @@ -3,7 +3,14 @@ ## Excluding controllers due to the problematic genetrack dependency ## Excluding job runners due to various external dependencies -python ./scripts/nosetests.py -v -w lib \ +COVERAGE=`which coverage` +COVERAGE_ARG="" +if [ $COVERAGE ]; then + COVERAGE_ARG="--with-coverage" +fi + +python ./scripts/nosetests.py -v \ + $COVERAGE_ARG \ --with-nosehtml --html-report-file run_unit_tests.html \ --with-doctest --exclude=functional --exclude="^get" \ - --exclude=controllers --exclude=runners + --exclude=controllers --exclude=runners lib test/unit diff -r dc6e0347edffb96fe4e633b362ad21a9f5a83e81 -r 682bc706f5d6c8caab7a46e405cdee158268c373 test/TESTING.md --- /dev/null +++ b/test/TESTING.md @@ -0,0 +1,7 @@ +Galaxy Testing +============== + +The Galaxy code base is large and contains many kinds of tests. Please +consult the [Galaxy +wiki](http://wiki.galaxyproject.org/Admin/Running%20Tests) for more +information on testing Galaxy. diff -r dc6e0347edffb96fe4e633b362ad21a9f5a83e81 -r 682bc706f5d6c8caab7a46e405cdee158268c373 test/unit/test_tool_loader.py --- /dev/null +++ b/test/unit/test_tool_loader.py @@ -0,0 +1,191 @@ +from tempfile import mkdtemp +from shutil import rmtree +import os + +from galaxy.util import parse_xml +from galaxy.tools.loader import template_macro_params, load_tool + +def test_loader(): + + class TestToolDirectory(object): + def __init__(self): + self.temp_directory = mkdtemp() + + def __enter__(self): + return self + + def __exit__(self, type, value, tb): + rmtree(self.temp_directory) + + def write(self, contents, name="tool.xml"): + open(os.path.join(self.temp_directory, name), "w").write(contents) + + def load(self, name="tool.xml", preprocess=True): + if preprocess: + loader = load_tool + else: + loader = parse_xml + return loader(os.path.join(self.temp_directory, name)) + + ## Test simple macro replacement. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <macro name="inputs"> + <inputs /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load(preprocess=False) + assert xml.find("inputs") is None + xml = tool_dir.load(preprocess=True) + assert xml.find("inputs") is not None + + # Test importing macros from external files + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <import>external.xml</import> + </macros> +</tool>''') + + tool_dir.write(''' +<macros> + <macro name="inputs"> + <inputs /> + </macro> +</macros>''', name="external.xml") + xml = tool_dir.load(preprocess=False) + assert xml.find("inputs") is None + xml = tool_dir.load(preprocess=True) + assert xml.find("inputs") is not None + + # Test macros with unnamed yield statements. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").find("input").get("name") == "first_input" + + # Test recursive macro applications. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + <expand macro="second" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + <macro name="second"> + <input name="second_input" /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").findall("input")[1].get("name") == "second_input" + + # Test recursive macro applications. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + <expand macro="second" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + <macro name="second"> + <expand macro="second_delegate" /> + </macro> + <macro name="second_delegate"> + <input name="second_input" /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").findall("input")[1].get("name") == "second_input" + + # Test <xml> is shortcut for macro type="xml" + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <xml name="inputs"> + <inputs /> + </xml> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs") is not None + + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <command interpreter="python">tool_wrapper.py + #include source=$tool_params + </command> + <macros> + <template name="tool_params">-a 1 -b 2</template> + </macros> +</tool> +''') + xml = tool_dir.load() + params_dict = template_macro_params(xml.getroot()) + assert params_dict['tool_params'] == "-a 1 -b 2" + + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <macros> + <token name="@CITATION@">The citation.</token> + </macros> + <help>@CITATION@</help> + <another> + <tag /> + </another> +</tool> +''') + xml = tool_dir.load() + help_el = xml.find("help") + assert help_el.text == "The citation.", help_el.text + + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <macros> + <token name="@TAG_VAL@">The value.</token> + </macros> + <another> + <tag value="@TAG_VAL@" /> + </another> +</tool> +''') + xml = tool_dir.load() + tag_el = xml.find("another").find("tag") + value = tag_el.get('value') + assert value == "The value.", value https://bitbucket.org/galaxy/galaxy-central/commits/71bd004a3354/ Changeset: 71bd004a3354 User: jmchilton Date: 2013-06-24 16:29:46 Summary: Update README.txt to reflect Python 2.5 is no longer supported. Affected #: 1 file diff -r 682bc706f5d6c8caab7a46e405cdee158268c373 -r 71bd004a3354b7132db03cb17b6a45997677e100 README.txt --- a/README.txt +++ b/README.txt @@ -7,7 +7,7 @@ HOW TO START ============ -Galaxy requires Python 2.5, 2.6 or 2.7. To check your python version, run: +Galaxy requires Python 2.6 or 2.7. To check your python version, run: % python -V Python 2.7.3 https://bitbucket.org/galaxy/galaxy-central/commits/6673bd3bf457/ Changeset: 6673bd3bf457 User: dannon Date: 2013-07-01 11:53:46 Summary: Merged in jmchilton/galaxy-central-multi-input-tool-fixes-2 (pull request #189) Small Unit Testing Improvements Affected #: 7 files diff -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 -r 6673bd3bf4571c4134797077ca85350a6319e444 .coveragerc --- /dev/null +++ b/.coveragerc @@ -0,0 +1,3 @@ +[run] +branch = True +include = lib/galaxy/* diff -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 -r 6673bd3bf4571c4134797077ca85350a6319e444 .hgignore --- a/.hgignore +++ b/.hgignore @@ -82,6 +82,9 @@ # Test output run_functional_tests.html test/tool_shed/tmp/* +.coverage +htmlcov +run_unit_tests.html # Project files *.kpf diff -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 -r 6673bd3bf4571c4134797077ca85350a6319e444 README.txt --- a/README.txt +++ b/README.txt @@ -7,7 +7,7 @@ HOW TO START ============ -Galaxy requires Python 2.5, 2.6 or 2.7. To check your python version, run: +Galaxy requires Python 2.6 or 2.7. To check your python version, run: % python -V Python 2.7.3 diff -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 -r 6673bd3bf4571c4134797077ca85350a6319e444 lib/galaxy/tools/loader.py --- a/lib/galaxy/tools/loader.py +++ b/lib/galaxy/tools/loader.py @@ -202,199 +202,3 @@ current_index += 1 parent_el.insert(current_index, deepcopy(target)) parent_el.remove(query) - - -def test_loader(): - """ - Function to test this module. Galaxy doesn't seem to have a - place to put unit tests that are not doctests. These tests can - be run with nosetests via the following command: - - % nosetests lib/galaxy/tools/loader.py - - """ - from tempfile import mkdtemp - from shutil import rmtree - - class TestToolDirectory(object): - def __init__(self): - self.temp_directory = mkdtemp() - - def __enter__(self): - return self - - def __exit__(self, type, value, tb): - rmtree(self.temp_directory) - - def write(self, contents, name="tool.xml"): - open(os.path.join(self.temp_directory, name), "w").write(contents) - - def load(self, name="tool.xml", preprocess=True): - if preprocess: - loader = load_tool - else: - loader = parse_xml - return loader(os.path.join(self.temp_directory, name)) - - ## Test simple macro replacement. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs" /> - <macros> - <macro name="inputs"> - <inputs /> - </macro> - </macros> -</tool>''') - xml = tool_dir.load(preprocess=False) - assert xml.find("inputs") is None - xml = tool_dir.load(preprocess=True) - assert xml.find("inputs") is not None - - # Test importing macros from external files - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs" /> - <macros> - <import>external.xml</import> - </macros> -</tool>''') - - tool_dir.write(''' -<macros> - <macro name="inputs"> - <inputs /> - </macro> -</macros>''', name="external.xml") - xml = tool_dir.load(preprocess=False) - assert xml.find("inputs") is None - xml = tool_dir.load(preprocess=True) - assert xml.find("inputs") is not None - - # Test macros with unnamed yield statements. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs"> - <input name="first_input" /> - </expand> - <macros> - <macro name="inputs"> - <inputs> - <yield /> - </inputs> - </macro> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs").find("input").get("name") == "first_input" - - # Test recursive macro applications. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs"> - <input name="first_input" /> - <expand macro="second" /> - </expand> - <macros> - <macro name="inputs"> - <inputs> - <yield /> - </inputs> - </macro> - <macro name="second"> - <input name="second_input" /> - </macro> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs").findall("input")[1].get("name") == "second_input" - - # Test recursive macro applications. - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs"> - <input name="first_input" /> - <expand macro="second" /> - </expand> - <macros> - <macro name="inputs"> - <inputs> - <yield /> - </inputs> - </macro> - <macro name="second"> - <expand macro="second_delegate" /> - </macro> - <macro name="second_delegate"> - <input name="second_input" /> - </macro> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs").findall("input")[1].get("name") == "second_input" - - # Test <xml> is shortcut for macro type="xml" - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <expand macro="inputs" /> - <macros> - <xml name="inputs"> - <inputs /> - </xml> - </macros> -</tool>''') - xml = tool_dir.load() - assert xml.find("inputs") is not None - - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <command interpreter="python">tool_wrapper.py - #include source=$tool_params - </command> - <macros> - <template name="tool_params">-a 1 -b 2</template> - </macros> -</tool> -''') - xml = tool_dir.load() - params_dict = template_macro_params(xml.getroot()) - assert params_dict['tool_params'] == "-a 1 -b 2" - - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <macros> - <token name="@CITATION@">The citation.</token> - </macros> - <help>@CITATION@</help> - <another> - <tag /> - </another> -</tool> -''') - xml = tool_dir.load() - help_el = xml.find("help") - assert help_el.text == "The citation.", help_el.text - - with TestToolDirectory() as tool_dir: - tool_dir.write(''' -<tool> - <macros> - <token name="@TAG_VAL@">The value.</token> - </macros> - <another> - <tag value="@TAG_VAL@" /> - </another> -</tool> -''') - xml = tool_dir.load() - tag_el = xml.find("another").find("tag") - value = tag_el.get('value') - assert value == "The value.", value diff -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 -r 6673bd3bf4571c4134797077ca85350a6319e444 run_unit_tests.sh --- a/run_unit_tests.sh +++ b/run_unit_tests.sh @@ -3,7 +3,14 @@ ## Excluding controllers due to the problematic genetrack dependency ## Excluding job runners due to various external dependencies -python ./scripts/nosetests.py -v -w lib \ +COVERAGE=`which coverage` +COVERAGE_ARG="" +if [ $COVERAGE ]; then + COVERAGE_ARG="--with-coverage" +fi + +python ./scripts/nosetests.py -v \ + $COVERAGE_ARG \ --with-nosehtml --html-report-file run_unit_tests.html \ --with-doctest --exclude=functional --exclude="^get" \ - --exclude=controllers --exclude=runners + --exclude=controllers --exclude=runners lib test/unit diff -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 -r 6673bd3bf4571c4134797077ca85350a6319e444 test/TESTING.md --- /dev/null +++ b/test/TESTING.md @@ -0,0 +1,7 @@ +Galaxy Testing +============== + +The Galaxy code base is large and contains many kinds of tests. Please +consult the [Galaxy +wiki](http://wiki.galaxyproject.org/Admin/Running%20Tests) for more +information on testing Galaxy. diff -r 9ddb3130b98d450ca2be3f447f171ff5f192b8a1 -r 6673bd3bf4571c4134797077ca85350a6319e444 test/unit/test_tool_loader.py --- /dev/null +++ b/test/unit/test_tool_loader.py @@ -0,0 +1,191 @@ +from tempfile import mkdtemp +from shutil import rmtree +import os + +from galaxy.util import parse_xml +from galaxy.tools.loader import template_macro_params, load_tool + +def test_loader(): + + class TestToolDirectory(object): + def __init__(self): + self.temp_directory = mkdtemp() + + def __enter__(self): + return self + + def __exit__(self, type, value, tb): + rmtree(self.temp_directory) + + def write(self, contents, name="tool.xml"): + open(os.path.join(self.temp_directory, name), "w").write(contents) + + def load(self, name="tool.xml", preprocess=True): + if preprocess: + loader = load_tool + else: + loader = parse_xml + return loader(os.path.join(self.temp_directory, name)) + + ## Test simple macro replacement. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <macro name="inputs"> + <inputs /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load(preprocess=False) + assert xml.find("inputs") is None + xml = tool_dir.load(preprocess=True) + assert xml.find("inputs") is not None + + # Test importing macros from external files + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <import>external.xml</import> + </macros> +</tool>''') + + tool_dir.write(''' +<macros> + <macro name="inputs"> + <inputs /> + </macro> +</macros>''', name="external.xml") + xml = tool_dir.load(preprocess=False) + assert xml.find("inputs") is None + xml = tool_dir.load(preprocess=True) + assert xml.find("inputs") is not None + + # Test macros with unnamed yield statements. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").find("input").get("name") == "first_input" + + # Test recursive macro applications. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + <expand macro="second" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + <macro name="second"> + <input name="second_input" /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").findall("input")[1].get("name") == "second_input" + + # Test recursive macro applications. + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs"> + <input name="first_input" /> + <expand macro="second" /> + </expand> + <macros> + <macro name="inputs"> + <inputs> + <yield /> + </inputs> + </macro> + <macro name="second"> + <expand macro="second_delegate" /> + </macro> + <macro name="second_delegate"> + <input name="second_input" /> + </macro> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs").findall("input")[1].get("name") == "second_input" + + # Test <xml> is shortcut for macro type="xml" + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <expand macro="inputs" /> + <macros> + <xml name="inputs"> + <inputs /> + </xml> + </macros> +</tool>''') + xml = tool_dir.load() + assert xml.find("inputs") is not None + + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <command interpreter="python">tool_wrapper.py + #include source=$tool_params + </command> + <macros> + <template name="tool_params">-a 1 -b 2</template> + </macros> +</tool> +''') + xml = tool_dir.load() + params_dict = template_macro_params(xml.getroot()) + assert params_dict['tool_params'] == "-a 1 -b 2" + + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <macros> + <token name="@CITATION@">The citation.</token> + </macros> + <help>@CITATION@</help> + <another> + <tag /> + </another> +</tool> +''') + xml = tool_dir.load() + help_el = xml.find("help") + assert help_el.text == "The citation.", help_el.text + + with TestToolDirectory() as tool_dir: + tool_dir.write(''' +<tool> + <macros> + <token name="@TAG_VAL@">The value.</token> + </macros> + <another> + <tag value="@TAG_VAL@" /> + </another> +</tool> +''') + xml = tool_dir.load() + tag_el = xml.find("another").find("tag") + value = tag_el.get('value') + assert value == "The value.", value Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits July 2013